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  1. Recently, Deep Learning based automatic generation of treatment recommendation has been attracting much attention. However, medical datasets are usually small, which may lead to over-fitting and inferior perfo...

    Authors: Chengkai Piao, Mengyue Lv, Shujie Wang, Rongyan Zhou, Yuchen Wang, Jinmao Wei and Jian Liu
    Citation: BMC Bioinformatics 2022 23:438
  2. In the context of a binary classification problem, the optimal linear combination of continuous predictors can be estimated by maximizing the area under the receiver operating characteristic curve. For ordinal...

    Authors: Priyam Das, Debsurya De, Raju Maiti, Mona Kamal, Katherine A. Hutcheson, Clifton D. Fuller, Bibhas Chakraborty and Christine B. Peterson
    Citation: BMC Bioinformatics 2022 23(Suppl 3):436

    This article is part of a Supplement: Volume 23 Supplement 3

  3. The aim of this study was to identify and screen long non-coding RNA (lncRNA) associated with immune genes in colon cancer, construct immune-related lncRNA pairs, establish a prognostic risk assessment model f...

    Authors: Zezhou Hao, Pengchen Liang, Changyu He, Shuang Sha, Ziyuan Yang, Yixin Liu, Junfeng Shi, Zhenggang Zhu and Qing Chang
    Citation: BMC Bioinformatics 2022 23:435
  4. Breast cancer is one of the most common cancers in women. It is necessary to classify breast cancer subtypes because different subtypes need specific treatment. Identifying biomarkers and classifying breast ca...

    Authors: Juntao Li, Hongmei Zhang and Fugen Gao
    Citation: BMC Bioinformatics 2022 23:434
  5. Increasing biomedical studies have shown that the dysfunction of miRNAs is closely related with many human diseases. Identifying disease-associated miRNAs would contribute to the understanding of pathological ...

    Authors: Ruiyu Guo, Hailin Chen, Wengang Wang, Guangsheng Wu and Fangliang Lv
    Citation: BMC Bioinformatics 2022 23:432
  6. Predicting morphological changes to anatomical structures from 3D shapes such as blood vessels or appearance of the face is a growing interest to clinicians. Machine learning (ML) has had great success driving...

    Authors: Joyce Zhanzi Wang, Jonathon Lillia, Ashnil Kumar, Paula Bray, Jinman Kim, Joshua Burns and Tegan L. Cheng
    Citation: BMC Bioinformatics 2022 23:431
  7. Studies have shown that classifying cancer subtypes can provide valuable information for a range of cancer research, from aetiology and tumour biology to prognosis and personalized treatment. Current methods u...

    Authors: Jiquan Shen, Jiawei Shi, Junwei Luo, Haixia Zhai, Xiaoyan Liu, Zhengjiang Wu, Chaokun Yan and Huimin Luo
    Citation: BMC Bioinformatics 2022 23:430
  8. Gene expression is regulated at different molecular levels, including chromatin accessibility, transcription, RNA maturation, and transport. These regulatory mechanisms have strong connections with cellular me...

    Authors: Surabhi Jagtap, Aurélie Pirayre, Frédérique Bidard, Laurent Duval and Fragkiskos D. Malliaros
    Citation: BMC Bioinformatics 2022 23:429
  9. Increasing evidence shows that circRNA plays an essential regulatory role in diseases through interactions with disease-related miRNAs. Identifying circRNA-disease associations is of great significance to prec...

    Authors: Lei Deng, Dayun Liu, Yizhan Li, Runqi Wang, Junyi Liu, Jiaxuan Zhang and Hui Liu
    Citation: BMC Bioinformatics 2022 23(Suppl 3):427

    This article is part of a Supplement: Volume 23 Supplement 3

  10. Age estimation from panoramic radiographs is a fundamental task in forensic sciences. Previous age assessment studies mainly focused on juvenile rather than elderly populations (> 25 years old). Most proposed ...

    Authors: Xuedong Wang, Yanle Liu, Xinyao Miao, Yin Chen, Xiao Cao, Yuchen Zhang, Shuaicheng Li and Qin Zhou
    Citation: BMC Bioinformatics 2022 23(Suppl 3):426

    This article is part of a Supplement: Volume 23 Supplement 3

    The Correction to this article has been published in BMC Bioinformatics 2022 23:557

  11. Cardiovascular disease (CVD) is a serious disease that endangers human health and is one of the main causes of death. Therefore, using the patient’s electronic medical record (EMR) to predict CVD automatically...

    Authors: Yanlong Qiu, Wei Wang, Chengkun Wu and Zhichang Zhang
    Citation: BMC Bioinformatics 2022 23(Suppl 8):425

    This article is part of a Supplement: Volume 23 Supplement 8

  12. RNA deleterious point mutation prediction was previously addressed with programs such as RNAmute and MultiRNAmute. The purpose of these programs is to predict a global conformational rearrangement of the secondar...

    Authors: Alexander Churkin, Yann Ponty and Danny Barash
    Citation: BMC Bioinformatics 2022 23(Suppl 8):424

    This article is part of a Supplement: Volume 23 Supplement 8

  13. Accurate precision approaches have far not been developed for modeling mortality risk in intensive care unit (ICU) patients. Conventional mortality risk prediction methods can hardly extract the information in...

    Authors: Fan Yang, Jian Zhang, Wanyi Chen, Yongxuan Lai, Ying Wang and Quan Zou
    Citation: BMC Bioinformatics 2022 23:423
  14. Despite continuing technological advances, the cost for large-scale genotyping of a high number of samples can be prohibitive. The purpose of this study is to design a cost-saving strategy for SNP genotyping. ...

    Authors: Camille Clouard, Kristiina Ausmees and Carl Nettelblad
    Citation: BMC Bioinformatics 2022 23:421
  15. Observational studies and Mendelian randomization experiments have been used to identify many causal factors for complex traits in humans. Given a set of causal factors, it is important to understand the exten...

    Authors: Zhuoran Ding, Marylyn D. Ritchie, Benjamin F. Voight and Wei-Ting Hwang
    Citation: BMC Bioinformatics 2022 23:420
  16. With the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving...

    Authors: Josh L. Espinoza and Chris L. Dupont
    Citation: BMC Bioinformatics 2022 23:419
  17. Gliomas are highly complex and heterogeneous tumors, rendering prognosis prediction challenging. The advent of deep learning algorithms and the accessibility of multi-omic data represent a new approach for the...

    Authors: Jing Tian, Mingzhen Zhu, Zijing Ren, Qiang Zhao, Puqing Wang, Colin K. He, Min Zhang, Xiaochun Peng, Beilei Wu, Rujia Feng and Minglong Fu
    Citation: BMC Bioinformatics 2022 23:417
  18. The advent of low cost, high throughput DNA sequencing has led to the availability of thousands of complete genome sequences for a wide variety of bacterial species. Examining and interpreting genetic variatio...

    Authors: Joshua D. Harling-Lee, Jamie Gorzynski, Gonzalo Yebra, Tim Angus, J. Ross Fitzgerald and Tom C. Freeman
    Citation: BMC Bioinformatics 2022 23:416
  19. Transcriptional regulation is a fundamental mechanism underlying biological functions. In recent years, a broad array of RNA-Seq tools have been used to measure transcription levels in biological experiments, ...

    Authors: Yiru Sheng, R. Ayesha Ali and Andreas Heyland
    Citation: BMC Bioinformatics 2022 23:415
  20. Accurate identification of protein complexes in protein-protein interaction (PPI) networks is crucial for understanding the principles of cellular organization. Most computational methods ignore the fact that ...

    Authors: Rongquan Wang, Caixia Wang and Huimin Ma
    Citation: BMC Bioinformatics 2022 23:414

    The Correction to this article has been published in BMC Bioinformatics 2022 23:494

  21. Biological age (BA) has been recognized as a more accurate indicator of aging than chronological age (CA). However, the current limitations include: insufficient attention to the incompleteness of medical data...

    Authors: Qing Yang, Sunan Gao, Junfen Lin, Ke Lyu, Zexu Wu, Yuhao Chen, Yinwei Qiu, Yanrong Zhao, Wei Wang, Tianxiang Lin, Huiyun Pan and Ming Chen
    Citation: BMC Bioinformatics 2022 23:411
  22. We used a hybrid machine learning systems (HMLS) strategy that includes the extensive search for the discovery of the most optimal HMLSs, including feature selection algorithms, a feature extraction algorithm,...

    Authors: Eskandar Taghizadeh, Sahel Heydarheydari, Alihossein Saberi, Shabnam JafarpoorNesheli and Seyed Masoud Rezaeijo
    Citation: BMC Bioinformatics 2022 23:410
  23. Artificial intelligence (AI) and machine learning (ML) have resulted in significant enthusiasm for their promise in healthcare. Despite this, prospective randomized controlled trials and successful clinical im...

    Authors: Julian C. Hong, Neville C. W. Eclov, Sarah J. Stephens, Yvonne M. Mowery and Manisha Palta
    Citation: BMC Bioinformatics 2022 23(Suppl 12):408

    This article is part of a Supplement: Volume 23 Supplement 12

  24. To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leverag...

    Authors: Yi Nian, Xinyue Hu, Rui Zhang, Jingna Feng, Jingcheng Du, Fang Li, Larry Bu, Yuji Zhang, Yong Chen and Cui Tao
    Citation: BMC Bioinformatics 2022 23(Suppl 6):407

    This article is part of a Supplement: Volume 23 Supplement 6

  25. Oxidative stress plays an important role in the progression of various types of tumors. However, its role in esophageal squamous cell carcinoma (ESCC) has seldom been explored. This study aimed to discover pro...

    Authors: Wei Liu, Hao-Shuai Yang, Shao-Yi Zheng, Hong-He Luo, Yan-Fen Feng and Yi-Yan Lei
    Citation: BMC Bioinformatics 2022 23:406
  26. Identifying protein complexes from protein-protein interaction network is one of significant tasks in the postgenome era. Protein complexes, none of which exceeds 10 in size play an irreplaceable role in life ...

    Authors: Jiaqing Lyu, Zhen Yao, Bing Liang, Yiwei Liu and Yijia Zhang
    Citation: BMC Bioinformatics 2022 23:405
  27. Bioinformatics has gained much attention as a fast growing interdisciplinary field. Several attempts have been conducted to explore the field of bioinformatics by bibliometric analysis, however, such works did...

    Authors: Jiaqi Wang, Zeyu Li and Jiawan Zhang
    Citation: BMC Bioinformatics 2022 23(Suppl 8):404

    This article is part of a Supplement: Volume 23 Supplement 8

  28. Microbes are associated with many human diseases and influence drug efficacy. Small-molecule drugs may revolutionize biomedicine by fine-tuning the microbiota on the basis of individual patient microbiome sign...

    Authors: Qiao Liu, Bohyun Lee and Lei Xie
    Citation: BMC Bioinformatics 2022 23(Suppl 3):403

    This article is part of a Supplement: Volume 23 Supplement 3

  29. In Alzheimer’s Diseases (AD) research, multimodal imaging analysis can unveil complementary information from multiple imaging modalities and further our understanding of the disease. One application is to disc...

    Authors: Yixue Feng, Mansu Kim, Xiaohui Yao, Kefei Liu, Qi Long and Li Shen
    Citation: BMC Bioinformatics 2022 23(Suppl 3):402

    This article is part of a Supplement: Volume 23 Supplement 3

  30. Population variant analysis is of great importance for gathering insights into the links between human genotype and phenotype. The 1000 Genomes Project established a valuable reference for human genetic variat...

    Authors: Tommaso Alfonsi, Anna Bernasconi, Arif Canakoglu and Marco Masseroli
    Citation: BMC Bioinformatics 2022 23:401
  31. Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate disc...

    Authors: E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Yodsawalai Chodpathumwan, Arash Termehchy, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman, Eric W. Deutsch, David Koslicki…
    Citation: BMC Bioinformatics 2022 23:400
  32. Twitter is a popular social networking site where short messages or “tweets” of users have been used extensively for research purposes. However, not much research has been done in mining the medical profession...

    Authors: Kazi Zainab, Gautam Srivastava and Vijay Mago
    Citation: BMC Bioinformatics 2022 22(Suppl 10):630

    This article is part of a Supplement: Volume 22 Supplement 10

  33. Protein histidine phosphorylation (pHis) plays critical roles in prokaryotic signal transduction pathways and various eukaryotic cellular processes. It is estimated to account for 6–10% of the phosphoproteome,...

    Authors: Jian Zhao, Minhui Zhuang, Jingjing Liu, Meng Zhang, Cong Zeng, Bin Jiang, Jing Wu and Xiaofeng Song
    Citation: BMC Bioinformatics 2022 23(Suppl 3):399

    This article is part of a Supplement: Volume 23 Supplement 3

  34. Brain volume has been widely studied in the neuroimaging field, since it is an important and heritable trait associated with brain development, aging and various neurological and psychiatric disorders. Genome-...

    Authors: Hung Mai, Jingxuan Bao, Paul M. Thompson, Dokyoon Kim and Li Shen
    Citation: BMC Bioinformatics 2022 23(Suppl 3):398

    This article is part of a Supplement: Volume 23 Supplement 3

  35. Advances in imagery at atomic and near-atomic resolution, such as cryogenic electron microscopy (cryo-EM), have led to an influx of high resolution images of proteins and other macromolecular structures to dat...

    Authors: Nathan Ranno and Dong Si
    Citation: BMC Bioinformatics 2022 23(Suppl 3):397

    This article is part of a Supplement: Volume 23 Supplement 3

  36. The eukaryotic genome is capable of producing multiple isoforms from a gene by alternative polyadenylation (APA) during pre-mRNA processing. APA in the 3′-untranslated region (3′-UTR) of mRNA produces transcri...

    Authors: Naima Ahmed Fahmi, Khandakar Tanvir Ahmed, Jae-Woong Chang, Heba Nassereddeen, Deliang Fan, Jeongsik Yong and Wei Zhang
    Citation: BMC Bioinformatics 2022 23(Suppl 3):396

    This article is part of a Supplement: Volume 23 Supplement 3

  37. Making clear what kinds of metabolic pathways a drug compound involves in can help researchers understand how the drug is absorbed, distributed, metabolized, and excreted. The characteristics of a compound suc...

    Authors: Zhihui Yang, Juan Liu, Hayat Ali Shah and Jing Feng
    Citation: BMC Bioinformatics 2022 23(Suppl 5):329

    This article is part of a Supplement: Volume 23 Supplement 5

  38. Microarrays can perform large scale studies of differential expressed gene (DEGs) and even single nucleotide polymorphisms (SNPs), thereby screening thousands of genes for single experiment simultaneously. How...

    Authors: Giuseppe Agapito, Marianna Milano and Mario Cannataro
    Citation: BMC Bioinformatics 2022 23(Suppl 6):393

    This article is part of a Supplement: Volume 23 Supplement 6

  39. Collagen VI family (COL6A) is a major member of extracellular matrix protein. There is accumulating evidence that COL6A is involved in tumorigenesis and tumor progression. In this study, we performed a systema...

    Authors: Xiang Li, Zeng Li, Shanzhi Gu and Xinhan Zhao
    Citation: BMC Bioinformatics 2022 23:390

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